The midafternoon announcement from Yahoo -1.62% followed a morning of media reports that Thompson would step down as a result of the furor over a false claim on his resume that he had a college degree in computer science.
It represented a major victory for Loeb.
AllThingsD dfirst reported Thompson’s impending departure.
Yahoo said Ross Levinsohn, the company’s head of head of global media, would replace Thompson as interim chief executive and Fred Amoroso would replace Bostock as chairman of the board.
The Wall Street Journal reported Thompson agreed to resign after the board of directors found evidence that contradicted his claim of innocence over his misstated academic record. The report cited unnamed people familiar with the matter.
The Journal and AllThingsD, like Forex Focus, the publisher of this report, are subsidiaries of News Corp.
Yahoo’s board is continuing its probe to determine if it can fire Thompson with cause, meaning he would forfeit millions in severance pay, the Journal said.
Yahoo also announced a settlement with Loeb of Third Point, the man who discovered the faked resume.
Loeb and allies Harry J. Wilson and Michael J. Wolf will join the board effective Wednesday, Yahoo said.
Yahoo said Bostock, and Patti Hart, VJ Joshi, Arthur Kern and Gary Wilson, all of whom previously said they wouldn’t stand for re-election, as well as Thompson have decided to step down from the board immediately.
Third Point, which owns 5.8% of Yahoo common stock, has agreed to withdraw its previous board nominations for consideration at the annual meeting and vote its shares in support of Yahoo’s nominees, the company said.
Yahoo’s slate for election or re-election at the 2012 annual meeting will include Amoroso, John Hayes, Peter Liguori, Thomas McInerney, Maynard Webb, Sue James, David Kenny, Brad Smith, Loeb, Wilson and Wolf.
Amoroso had been leading a probe into how the phony credentials were put in Thompson’s biography and ended up in the company’s regulatory filings.
The company’s full board met on Sunday to hammer out a final deal, AllThingsD said.
As part of the agreement, Loeb will drop his proxy fight, the Journal reported.
Thompson’s resume had said he had degrees in computer science and accounting from Stonehill College in Easton, Mass., when he actually only had an accounting degree. He reportedly graduated in 1979.
He had at first called the resume problem a “distraction” and an “inadvertent error” after news of it broke 10 days ago. He also attempted to blame a search firm for it.
Thompson took the top job in January after the firing of former CEO Carol Bartz in September 2011. The company has been overseen by four CEOs, including Terry Semel and co-founder Jerry Yang, since 2007.
Thompson had previously been at eBay -1.14% , where he was president of the company’s PayPal unit. His biography on eBay’s site had also said that he had a computer-science degree, although the company’s filings with the SEC were accurate.
The controversy had already claimed one member of Yahoo’s board last week when Hart, who chaired the committee that tapped Thompson, stepped down. Hart is chief executive of slot machine maker International Game Technology +1.54% .